@dalehileman,
Why is it troublesome? This is math, not philosophy.
0 is just a number. Does it trouble you that at some point the object thrown upward is traveling at a speed of 2 m/s (for the same "zero duration") and soon after at a speed of 1.8 m/s?
A ball thrown upward at 29.4 m/s (a number I chose to make the calculation easy but any number will work). Every second it will be going 9.8 m/s slower (i.e. we subtract 9.8 m/s from its speed).
After 1 second it will be going 19.6 m/s upward (I just subtracted 9.8 m/s from the original speed.
After 2 seconds it will be going 9.8 m/s upward (again I just subtracted another 9.8 m/s)
After 3 seconds it will be going 0 m/s (Yes 0 m/s means stopped)
After 4 seconds it will be going -9.8 m/s upward which is the same as 9.8 m/s downward (again I simply subtracted 9.8m/s).
After 5 seconds it will be going 19.6 m/s downward.
There is nothing complicated or mystical about this. This has nothing to do with relativity or anything you couldn't understand with what you learned in a standard high school science class.
It is simply the definition of acceleration. An acceleration of -9.8 m/s/s means that every second you subtract 9.8 m/s from the speed.
As you see from the example above, 0m/s is quite easy to hit. It shouldn't surprise you. After all 0 is just a number and a speed of 0 m/s is no more surprising than any other speed (like 2 m/s, or 100 m/s).